Before you can appreciate sections through the brain,
you need to know the planes of orientation. There are three types
of sections: coronal, horizontal, and sagittal. They are diagrammed
below.

Coronal sections are the easiest to visualize, because
their orientation is just like looking face-on at another person.
Up is up and down is down. We will start with the most rostral
sections, or those closest to the nose.

Note: these
sections have not been cut on a perfectly coronal plane, and are
in fact tilted backwards a little. They will differ slightly
from the pictures found in the DeArmond atlas. However, the relationships
between structures are unchanged.

The very first section you would see in a coronal
series would be just the tips of the frontal lobes, which sit
right behind the forehead. We have skipped forward a little to
the first section containing internal structures. These slides
have been stained for myelin, which makes all of the white
matter (axons) black. The grey matter (cell bodies)
appears white. Paradox? The grey and white matter were originally
named for their appearance in freshly cut brain tissue. Myelinated
axons, with their high fatty content, look whiter than cell bodies.

The first thing to notice is the corpus callosum. This major highway connecting the two hemispheres will serve as a useful landmark, because it appears in all coronal sections. The color of the corpus callosum will also tell you the color of white matter, which can vary with the type of stain. In these sections, white matter is black.

Below the corpus callosum you can see the tips of the two lateral ventricles. They are separated by a thin septum which carries a second set of axons, the fornix. The fornix is

carrying information from the hippocampi to the mamillary bodies, and travels along the midline from back to front. It does not cross the midline like the corpus callosum, however.

Notice the lumps of grey matter sitting in the lateral
ventricles. These are the caudate nuclei, and the rule
for identifying them is simple: if you can see lateral ventricles,
you can see caudate. This applies throughout the curved extent
of the lateral ventricles - the caudate follows them the whole
way.

The caudate appears to blend into another nucleus
(a nucleus is any collection of cell bodies), the putamen.
These two nuclei are almost always divided by a band of axons
called the internal capsule. But here in the rostral brain,
you can see that the two are continuous at their bases. In reality,
the caudate and the putamen are all one nucleus, which was coincidentally
cut in half by the internal capsule. Early anatomists didn't
realize this, so they were named separately, and the small bridge
which connects them ventromedially was named the nucleus accumbens.
All three nuclei are sometimes collectively called the striatum,
however, to acknowledge their continuity.

You can also see the beginnings of a dark nucleus
medial to the putamen. This nucleus has a lot of axons in it,
so in fresh-cut brain it appears very pale. Hence it is named
the globus pallidus.

In the next most caudal section, some things have changed. Notice that the nucleus accumbens is gone and the caudate and putamen are no longer connected. There is also a moustache-like tract crossing from right to left. This is the anterior commissure, and represents one of only two major tracts that connect the hemispheres. The other is the corpus callosum. The posterior commissure, which connects the left and right midbrain, is small and hard to find.

In the next section, we see the arrival of another major player, the thalamus. The thalamus is really a heterogeneous group of nuclei, but they all share the

same basic function - they are the gatekeeper for anything that wants to get up to cortex. The thalamic nuclei are located on either side of the slit-like third ventricle. This gives us another rule: if you can see third ventricle, you can see thalamus. Sometimes the thalamus will send a little bridge across the third ventricle, appearing to create two smaller ventricles. This is a normal anatomic variant. Notice that the thalamus sits on top of the internal capsule, while the putamen and globus pallidus remain below -

this relationship is always preserved.

Speaking of the globus pallidus, in this section
it begins to look like two nuclei. The outer shell is now called
the globus pallidus externa, while the inner wedge is the
globus pallidus interna.

The optic chiasm is visible here, hanging
down below the base of the brain. It will split to form the optic
tracts, which will burrow up into the brain. These pathways
are carrying all of the information from the eyes.

In the next section, the globus pallidus and putamen are beginning to recede, and the thalamus is increasing in size. The optic tracts are entering the brain. A new structure visible here is the amygdala. The amygdala is one of two major structures which are found on the medial surface of the temporal lobe (the other is the hippocampus). The amygdala has a characteristic marbled appearance in these sections, due to the axons winding through it. It is part of the limbic system,

and deals with the emotional significance of experiences.

This is the last section of this series, and a lot
has changed. The lateral ventricle is visible in two places.
The lateral ventricle, like many other structures in the brain,
curves back and loops under itself like a big C. Therefore, in
some parts of the brain you can cut it in two places. The caudate
follows this curve, so it can also be seen in two places.

The hippocampus has taken the place of the amygdala. The hippocampus, which looks distinctly like a jellyroll, is involved in memory formation and will be the subject of later sections.

In the center of this section, things look radically different. We are at the junction of brainstem and cerebrum, which is called the midbrain. The midbrain can be identified by two major landmarks: the cerebral aqueduct, which is the narrow channel between the third and fourth ventricles, and the

cerebral peduncles. The cerebral peduncles are really a continuation of the internal capsule - move back one section and notice how it begins to stream down towards the base of the brain. The peduncles are quite literally the "stalk" of the cerebrum, and all of the axons passing up to or down from the brain are carried in them.

Just lateral to the peduncles are a pair of structures
involved in vision, the lateral geniculate nuclei. They
have a typical layered, peaked shape, and are the target of the
optic tract. Right above the peduncles you can see the pale substantia
nigra. The substantia nigra produces dopamine, and is critical
for normal movement; Parkinson's disease is the degeneration
of this nucleus. A byproduct of the production of dopamine, neuromelanin,
accumulates with age and makes it look dark in fresh-brain preparations.
This explains the name substantia nigra ("black stuff").

Above the substantia nigra are two perfectly round
circles. These are the red nuclei (you guessed it, due
to their appearance in fresh brain), which are involved with the
cerebellum. They are another landmark of the midbrain, and the
trio of peduncles, substantia nigra, and red nuclei are almost
always found together.

Finally, we have the remains of the thalamus. This
caudal-most extension of thalamus hangs over the midbrain and
is called the pulvinar.

B. Horizontal sections:

Horizontal sections are often used clinically, as
MRI and CT scans are taken in the horizontal plane. In these
horizontal sections we will start at the top of the brain and
cut sections downward. In the pictures, rostral (the nose) is
up.

Due to the unique curvatures of the brain, the relative locations of nuclei in horizontal cuts are strikingly similar to what you saw in coronal sections. For example, in this section, lateral ventricles can be found just under the corpus callosum, caudate can be found in the lateral ventricles, and putamen is separated from caudate by the internal capsule. There are some noticeable differences, however. First, you can see the full extent of the lateral ventricles, front to back. Second, you can see a large posterior fiber tract crossing from right to left. The posterior commissure? No, too big. This is part of the corpus callosum. The corpus callosum is U-shaped in cross section, but from the side it also curves like a C. In horizontal section, we

cut through it twice. Third, the true shape of the internal capsule is revealed in horizontal section - it is V-shaped. It has an anterior limb and a posterior limb; the latter carries most of the pathways we will learn about later.

Both thalamus and fornix are visible here, and since they make the walls and the roof of the third ventricle, respectively, we must be about to cut through third ventricle.

In the next section we can indeed see the third ventricle and the thalamic nuclei on either side. The channel between the lateral ventricles and the third ventricle is visible, the foramen of Monro. The globus pallidus has appeared just where it should, nestled inside the putamen. We are beginning to lose the rostral part of the corpus callosum. The thalamus is very large in this section.

In this last section we have cut all the way down to the midbrain. The midbrain appears upside down; remember that the peduncles are pointing towards your throat, so they will point down in coronal section but up in a horizontal section. Otherwise, all of the midbrain landmarks look pretty similar; you can see peduncles, substantia nigra, and red nuclei, along with the lateral geniculate (LGN) and its partner, the medial geniculate (MGN). The MGN is part of the auditory pathway, while the LGN is visual. The cerebellum, which sits at the back of the brain and coordinates movement, has been barely nicked in this section.

Now that you are familiar with the major structures
and their relationships, look through either an atlas or a neuroanatomy
program and try to identify them without labels. Remember that
the plane of section may vary slightly - for example, the optic
chiasm may appear in the same section as the anterior commissure.
You should still be able to identify structures based on their
shape (such as the LGN), their appearance (the scrolled hippocampus),
or their relationship to the ventricles (the caudate and thalamus).